Nfkb1 Removal from Proximal Tubule Cells Improves Renal Tubular Outcomes Following Ischemia Reperfusion Injury

KEY POINTS: Persistent NF-κB signaling associates within injured proximal tubule cells (PTCs) that fail to repair on kidney injury. Removing activity of Nfkb1, a transcriptional effector of NF-κB signaling, in PTCs enhances PTC repair and decreases injury associated fibrosis. Coexpression of Nfkb1 and Relb in injured PTCs suggests additional improvement from comprehensive targeting of NF-κB transcriptional regulators. BACKGROUND: CKD is a significant global health burden. AKI is a risk factor of progression to CKD. Recent studies have linked failure in proximal tubule repair as a potential contributing factor to CKD in mouse and human studies. Failed repair proximal tubule cells (FR-PTCs), initially presenting at the site of maximal sensitivity to ischemia reperfusion injury and spreading to more cortical regions over time, adopt a senescence-associated secretory phenotype linked to activation of the NF-kB pathway. Several transcriptional regulatory factors mediate NF-kB pathway action. Of these, Nfkb1 is prominent within FR-PTCs and chromatin studies predict Nfkb1 interactions with pathology-associated gene targets. METHODS: To examine the role of NF-kB in nephron injury outcomes, we removed Nfkb1 activity within the nephron lineage of the mouse kidney and examined the kidney's response to bilateral ischemia reperfusion injury. RESULTS: Single-cell transcriptional analysis showed a significant reduction of inflammation-associated gene expression, including Ccl2, Birc3, Spp1, Cd47, and Traf1, in Nfkb1-deficient FR-PTCs. A reduced pathological signature correlated with normalized expression of genes associated with healthy proximal tubule function, including Cubn, Kap, and a number of solute carriers. Single-nucleus Assay for Transposase-Accessible Chromatin seq analysis linked transcriptomic changes to enhancer regulation, particularly marked opening of chromatin for targets of hepatocyte nuclear factor family members associated with normal regulation of gene expression in proximal tubule cells. CONCLUSIONS: Examining Assay for Transposase-Accessible Chromatin seq motif predictions and performing direct immunolabeling studies suggested Relb, another transcriptional mediator of NF-κB transcriptional responses with overlapping targeting specificity to Nfkb1, may partially compensate for the loss of Nfkb1. These studies support future efforts to remove ongoing NF-κB signaling within nephrons as a potential therapeutic strategy to target the AKI-to-CKD transition.